Enable searching on obsolete terms

[hdrabkin]

It would be useful to be able to search for an obsolete term on the landing page. For example, if there is an obsolete term, I could ask ' show me all models/annotations that have an annotation to a term that has been obsoleted. ' This is important for the times that we fall behind the deadline time table for the spreadsheet reviews

[vanaukenk]

See also: https://github.com/geneontology/noctua/issues/788

[kltm]

@tmushayahama I think adding the following fq fixes this: OR is_obsolete:true I.e.: http://noctua-golr.berkeleybop.org/select?defType=edismax&indent=on&qt=standard&wt=json&rows=50&start=0&packet=1&callback_type=search&qf=annotation_class^3&qf=annotation_class_label_searchable^5.5&qf=description_searchable^1&qf=comment_searchable^0.5&qf=synonym_searchable^1&qf=alternate_id^1&qf=isa_closure^1&qf=isa_closure_label_searchable^1&_=1682010874400&fq=document_category:%22ontology_class%22&fq=isa_closure:%22GO:0003674%22%20OR%20isa_closure:%22GO:0008150%22%20OR%20isa_closure:%22GO:0005575%22%20OR%20isa_closure:%22GO:0044848%22%20OR%20isa_closure:%22CARO:0000000%22%20OR%20isa_closure:%22CL:0000003%22%20OR%20isa_closure:%22UBERON:0000105%22%20OR%20is_obsolete:true&q=obsol*&json.wrf=ng_jsonp_callback_0

[tmushayahama]

@kltm Thank you, yes it works now

[ukemi]

Something weird is happening with the search results. I searched on 'obsolete regulation of cell death' from the landing page on Noctua-dev. The search returned models that look like they have nodes that USED TO BE children of this term. For example:

• The search returns gomodel:60418ffa00001019 which has 'regulation of programmed cell death' nodes.
• The search returns gomodel:5ce58dde00001215 which has a 'negative regulation of intrinsic apoptotic signaling pathway' node.
• The search returns gomodel:613aae0000000813 which has 'negative regulation of hepatocyte apoptotic process' nodes.

This is strange behavior because these terms should no longer be is_a children of an obsolete term. Is there a synchronization issue on Noctua-dev?

[vanaukenk]

Tested again on 2023-05-18 Noctua workbenches call. Updating the ontology on noctua-dev fixed the issue @ukemi reported above. Searching for an obsolete term now returns the expected results. Okay to move into production.